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First published online 4 March 2003
doi: 10.1242/jcs.00352

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Genome-wide expression screens indicate a global role for protein kinase CK2 in chromatin remodeling

Biochemische Zellphysiologie (B0200) and Intelligente Bioinformatiksysteme (H0900), Deutsches Krebsforschungszentrum, 69120 Heidelberg, Germany

View larger version (32K): [in a new window]   Fig. 1. Correspondence analysis graphs illustrating the dependencies of gene expression profiles during the early cell cycle of CK2 deletion strains. Transcript profiles of -factor-synchronized yeast strains were determined at 0, 7 and 14 minutes after pheromone release by hybridization to oligonucleotide arrays across the whole yeast genome. Expression specificities of single genes can be detected by their distance from the center and the direction of the corresponding condition. (A) ckb1 ckb2 strain compared with the wildtype. (B) cka1 strain compared with the wildtype. (C) cka2 strain compared with the wildtype. Note that CK2 mutants were constructed by gene disruption techniques. Thus, although fractional transcription of deleted CK2 subunit genes results in no functioning proteins, weak transcript signals are detected on oligonucleotide arrays, and their distance from the center is not as far as one might expect.

View larger version (18K): [in a new window]   Fig. 2. Cell-cycle-regulated genes affected in early cell cycle expression by perturbation of protein kinase CK2. Significantly deviating expression was defined as having at least a two-fold difference in transcription levels compared with the wildtype. (A) A Venn diagram showing numbers of deviating genes at at least one time point in the different CK2 subunit deletion strains. (B) Time point distribution of genes altered in at least one of the CK2 mutants.

View larger version (14K): [in a new window]   Fig. 3. Phase-specific distribution of altered cell cycle genes in the CK2 mutants. (A) Pie chart showing total numbers of genes altered at cell cycle entry according to peak expression. (B) Number of genes showing expression deviations in asynchronous CK2 mutant cultures according to peak expression. Black sections contain genes peaking at multiple phases.

View larger version (11K): [in a new window]   Fig. 4. Cell-cycle-regulated genes showing persistent expression deviations in CK2 deletion strains. Venn diagram showing CK2-mutant-specific distribution of genes altered in the early cell cycle and asynchronous cultures.

View larger version (28K): [in a new window]   Fig. 5. Effects of CK2 perturbation at cell cycle entry on expression of cell-cycle-regulated genes. When (re-)entering the cell cycle following factor arrest (a differentiated, G0-like state), CK2 mutants show significant expression deviations for genes specific for all cell cycle stages. Affected genes are positioned in boxes according to their phase-specific peak expression. Genes are functionally linked to the SPB, TOS (topoisomerase 2), CHR, (chromatin remodeling) and CCC (cell cycle control).